SeqAn3
The Modern C++ library for sequence analysis.
seqan3::sequence_file_input_traits Interface Reference

The requirements a traits_type for seqan3::sequence_file_input must meet. More...

#include <seqan3/io/sequence_file/input.hpp>

+ Inheritance diagram for seqan3::sequence_file_input_traits:

Related Functions

(Note that these are not member functions.)

Requirements for seqan3::sequence_file_input_traits

You can expect these member types of all types that satisfy seqan3::sequence_file_input_traits.

Note that the alphabet type of the seqan3::field::seq_qual cannot be specified directly, it is always seqan3::qualified<sequence_alphabet, quality_alphabet> and the container type templates for the field are those of seqan3::field::seq.

using sequence_alphabet
 Alphabet of the characters for the seqan3::field::seq; must satisfy seqan3::alphabet.
 
using sequence_legal_alphabet
 Intermediate alphabet for seqan3::field::seq; must satisfy seqan3::alphabet and be convertible to sequence_alphabet. More...
 
using sequence_container
 Type template of the seqan3::field::seq, a container template over sequence_alphabet; must satisfy seqan3::sequence_container.
 
using id_alphabet
 Alphabet of the characters for the seqan3::field::id; must satisfy seqan3::alphabet.
 
using id_container
 Type template of the seqan3::field::id, a container template over id_alphabet; must satisfy seqan3::sequence_container.
 
using quality_alphabet
 Alphabet of the characters for the seqan3::field::qual; must satisfy seqan3::writable_quality_alphabet.
 
using quality_container
 Type template of the seqan3::field::qual, a container template over quality_alphabet; must satisfy seqan3::sequence_container.
 

Detailed Description

The requirements a traits_type for seqan3::sequence_file_input must meet.

Friends And Related Function Documentation

◆ sequence_legal_alphabet()

using sequence_legal_alphabet
related

Intermediate alphabet for seqan3::field::seq; must satisfy seqan3::alphabet and be convertible to sequence_alphabet.

This alphabet can be a superset of sequence_alphabet to allow conversion of some characters without producing an error, e.g. if this is set to seqan3::dna15 and sequence_alphabet is set to seqan3::dna5, 'M' will be an accepted character and automatically converted to 'N', while 'Z' will still be an illegal character and produce an error.


The documentation for this interface was generated from the following file: